TY - JOUR
T1 - Differentiating the protein coding and noncoding rna segments of dna using shannon entropy
AU - Mazaheri, P.
AU - Shirazi, A. H.
AU - Saeedi, N.
AU - Reza Jafari, G.
AU - Sahimi, Muhammad
PY - 2010/1
Y1 - 2010/1
N2 - The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacterium Clostridium difficile 630 (G + C = 29.1%) and Bdellovibrio bacteriovorus (G + C = 50.6%) are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content, ΔrS - the relative difference of the two entropies - is significantly greater in protein-coding regions, when compared with noncoding RNA segments.
AB - The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacterium Clostridium difficile 630 (G + C = 29.1%) and Bdellovibrio bacteriovorus (G + C = 50.6%) are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content, ΔrS - the relative difference of the two entropies - is significantly greater in protein-coding regions, when compared with noncoding RNA segments.
KW - DNA Sequence
KW - Shannon Entropy
UR - http://www.scopus.com/inward/record.url?scp=77951582193&partnerID=8YFLogxK
U2 - 10.1142/S0129183110014975
DO - 10.1142/S0129183110014975
M3 - Article
AN - SCOPUS:77951582193
SN - 0129-1831
VL - 21
SP - 1
EP - 9
JO - International Journal of Modern Physics C
JF - International Journal of Modern Physics C
IS - 1
ER -